catalog_gwas_pliercanon_sep_ldclumping_r01d1000_adipose

Last updated: 2020-11-21

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Introduction

The analysis in this part is the same with PLIER-Canonical. But in this part, I used Adipose Subcutaneous expression data. It contains 581 samples.

Material and Methods

This part is the same with PLIER-Canonical.

Snps after filter

After filtering by ‘pval < 5e-8’ and LD Clumping, for each trait, I got :

platelet count trait contains 691 SNPs with pval<5e-8.

white blood cell count trait contains 367 SNPs with pval<5e-8.

myeloid white cell count trait contains 317 SNPs with pval<5e-8.

lymphocyte count trait contains 446 SNPs with pval<5e-8.

red blood cell count trait contains 462 SNPs with pval<5e-8.

granulocyte count trait contains 308 SNPs with pval<5e-8.

eosinophil count trait contains 496 SNPs with pval<5e-8.

neutrophil count trait contains 311 SNPs with pval<5e-8.

IBD trait contains 118 SNPs with pval<5e-8.

Ulcerative colitist trait contains 75 SNPs with pval<5e-8.

Crohn’s disease trait contains 97 SNPs with pval<5e-8.

BMI trait contains 102 SNPs with pval<5e-8.

T2D contains 14 SNPs with pval<5e-8. T2D_2 contains 4 SNPs with pval<5e-8.

Asthma trait contains 192 SNPs with pval<5e-8. Asthma_2 trait contains 110 SNPs with pval<5e-8.

HDL trait contains 225 SNPs with pval<5e-8.

LDL trait contains 203 SNPs with pval<5e-8.

WHR trait contains 37 SNPs with pval<5e-8.

Results - pval < 5e-8 & 120 PEER factors & covariants: 10 PCs + GTEx:Sequencing platform,Sequencing protocol,Sex + AGE

Summary table

I used ‘qvalue’ R package to compute the fdr from p-values for each SNP and made a table to show the number of SNPs that pass the threshold. The thresholds are ‘fdr < 0.1’,‘fdr < 0.2’,‘pval < 5e-8’. The ‘num_significant_pairs’ indicates the number of significant pairs under each threshold. If a trait~factor pair has as least 1 significant SNP, we named it as ‘significant pair’.

Info table

For each trait, I made a table to show the info of snps with fdr>0.2 in the factor ~ SNP + genotype pcs association test. For each trait,The LVs have more than one significant SNPs with FDR<0.2 are included.

The suffix ’_assoc’ here means that results are from factor ~ SNP + genotype pcs association test. The suffix ’_gwas’ here means results are from original GWAS results files. For EUR.CD, EUR.IBD, EUR.UC, the effectsize_gwas here means ‘ln(OR)’, for others, it means ‘beta’.

‘snp_ld’ here means the snps that in LD with the snp in each line.’ld_r2’ means the LD r-squared which is corresponding to the ‘snp_ld’ column. ‘cis-eqtl’ column indicates whether the snp is a cis-eqtl according to GTEx data. ‘cis_gene_hgnc’ and ‘cis_gene_hgnc’ is the genes that the snp influence when it act as cis-eqtl. ‘func’ and ‘func_gene’ are obtained from ANNOVAR, which indicating the snp function within the genes.

Enrichment analysis

Eocinophil/granulocyte count/neutrophil count/lymphocyte count/myeloid white cell count - LV74

Eocinophil - LV84

Eocinophil - LV121

Ulcerative colitist - LV29

LDL - LV35

Warning in instance$preRenderHook(instance): It seems your data is too big
for client-side DataTables. You may consider server-side processing: https://
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Red Blood Cell Count - LV104

Effect size plots

For each trait, I made a plot of association with LV(indicating by beta in GWAS) vs association with trait(indicating by ln(odds ratio) or beta in GWAS) to show if the variants have the correlated effect direction. The effect sizes of Catalog GWAS and factor association tests are harmonized by TwoSampleMR R package to make the effect alleles in these two analysis identical. The LVs have more than one significant SNPs with FDR<0.2 are included in the plotting.Besides, for each plots, I fitted the points with intercept = 0. The pvalues and r-squared are shown on the plots.

Asthma_2

None of the LVs have >1 SNPs at FDR<0.2.

BMI

Eosinophil count

Crohn’s disease

IBD

Ulcerative colitist

granulocyte count

HDL

None of the LVs have >1 SNPs at FDR<0.2.

LDL

lymphocyte count

myeloid white cell count

neutrophil count

plt

rbc

T2D_2

None of the LVs have >1 SNPs at FDR<0.2.

T2D

None of the LVs have >1 SNPs at FDR<0.2.

asthma

wbc

None of the LVs have >1 SNPs at FDR<0.2.

eo

None of the LVs have >1 SNPs at FDR<0.2.

Resampling

For some promising trait-factor pairs, I did resampling. I resampled the SNPs without replacement, I fitted the points with intercept = 0 again and recorded the pvalues and r-squared. The resampling was repeated 1000 times. The following plots are the resampling results.

I made a histogram to show the pvalues/rsquared distribution from resampling. The red line in the plots are the pvalue/rsquared in the origin analysis. The p_mean/r_mean values in the plots are the mean values of the resampling. The ‘prob of getting more extreme values’ is computed by: (number of more extreme values)/(times of resampling)

Eosinophil count

Ulcerative colitist

granulocyte count

LDL

lymphocyte count

neutrophil count

myeloid white cell count

red blood cell count

Effect size plots- more SNPs

For some promising trait-factor pairs , I relaxed the fdr threshold of the SNPs that used to make effect size plots(from 0.2 to 0.3/0.5)

Eosinophil count

Ulcerative colitist

granulocyte count

LDL

lymphocyte count

neutrophil count

myeloid white cell count

red blood cell count

Effect size plots - checking the reverse causality

To check if the effect size correlation is due to reverse causality: i.e. trait -> LV (trait causally affect LV), instead of LV -> trait (which is what we like to see). I used all SNPs associated with traits(pval<5E-8). The x-axis is the effects of these SNPs on trait, and y-axis is the effects on LV.

Some pair show p < 0.05, the result may be driven by the possible causal effect of LV -> trait. To test this, I removed the SNPs that are associated with LVs at FDR < 0.2 and made the plots again.

Eosinophil count

Ulcerative colitist

granulocyte count

LDL

lymphocyte count

neutrophil count

myeloid white cell count

red blood cell count

QQplots - promising pairs

Eosinophil count

Ulcerative colitist

granulocyte count

LDL

lymphocyte count

neutrophil count

myeloid white cell count

red blood cell count

Colocalization

The colocalization analysis was performed using the approximate Bayes factor test implemented in the Coloc package. Coloc computes five posterior probabilities (PP0, PP1, PP2, PP3 and PP4), each corresponding to a hypothesis: H0, no association with either trait; H1, association with trait 1 but not with trait 2; H2, association with trait 2 but not with trait 1; H3, association with trait 1 and trait 2, two independent SNPs; H4, association with trait 1 and trait 2, one shared SNP. We ran Coloc with the default parameters and used PP4 to assess evidence of colocalization. We visualized the colocalization of factor - QTLs and GWAS associations using the LocusCompareR package.

Chromosome selection: I first sorted the SNPs by their pvalues from factor association tests, then I selected the first two SNPs and chose their chromosome to do the colocalization test adn visualization.

Eosinophil count

LV74

pvalues in coloclization
		note
nsnps	654	NA
PP.H0.abf	4.32951012214208e-15	no association with either trait
PP.H1.abf	1.47039883050559e-14	association with trait 1 but not with trait 2
PP.H2.abf	0.012147306446318	association with trait 2 but not with trait 1
PP.H3.abf	0.0403074343772307	association with trait 1 and trait 2,two independent SNPs
PP.H4.abf	0.947545259176435	association with trait 1 and trait 2, one shared SNP

pvalues in coloclization
		note
nsnps	551	NA
PP.H0.abf	4.51503740879928e-15	no association with either trait
PP.H1.abf	1.49802568801237e-14	association with trait 1 but not with trait 2
PP.H2.abf	0.0109205471062468	association with trait 2 but not with trait 1
PP.H3.abf	0.035279033577639	association with trait 1 and trait 2,two independent SNPs
PP.H4.abf	0.953800419316093	association with trait 1 and trait 2, one shared SNP

pvalues in coloclization
		note
nsnps	587	NA
PP.H0.abf	1.30154749414775e-21	no association with either trait
PP.H1.abf	9.73567901978272e-22	association with trait 1 but not with trait 2
PP.H2.abf	0.0301083403492439	association with trait 2 but not with trait 1
PP.H3.abf	0.0215729599148834	association with trait 1 and trait 2,two independent SNPs
PP.H4.abf	0.948318699735872	association with trait 1 and trait 2, one shared SNP

pvalues in coloclization
		note
nsnps	100	NA
PP.H0.abf	0.895363538820831	no association with either trait
PP.H1.abf	0.0964494552470313	association with trait 1 but not with trait 2
PP.H2.abf	0.00366956720683393	association with trait 2 but not with trait 1
PP.H3.abf	0.00039116317140931	association with trait 1 and trait 2,two independent SNPs
PP.H4.abf	0.00412627555389428	association with trait 1 and trait 2, one shared SNP

pvalues in coloclization
		note
nsnps	151	NA
PP.H0.abf	0.909990082714903	no association with either trait
PP.H1.abf	0.0806086328367058	association with trait 1 but not with trait 2
PP.H2.abf	0.00549203403761318	association with trait 2 but not with trait 1
PP.H3.abf	0.000483068521375786	association with trait 1 and trait 2,two independent SNPs
PP.H4.abf	0.00342618188940235	association with trait 1 and trait 2, one shared SNP

lv84

pvalues in coloclization
		note
nsnps	633	NA
PP.H0.abf	0.520867968468262	no association with either trait
PP.H1.abf	0.219558425612122	association with trait 1 but not with trait 2
PP.H2.abf	0.0163221224603899	association with trait 2 but not with trait 1
PP.H3.abf	0.00664356080914982	association with trait 1 and trait 2,two independent SNPs
PP.H4.abf	0.236607922650077	association with trait 1 and trait 2, one shared SNP

pvalues in coloclization
		note
nsnps	670	NA
PP.H0.abf	9.52195421752099e-90	no association with either trait
PP.H1.abf	1.96819913996693e-90	association with trait 1 but not with trait 2
PP.H2.abf	0.693469246408423	association with trait 2 but not with trait 1
PP.H3.abf	0.143177555947148	association with trait 1 and trait 2,two independent SNPs
PP.H4.abf	0.163353197644415	association with trait 1 and trait 2, one shared SNP

lv121

pvalues in coloclization
		note
nsnps	836	NA
PP.H0.abf	0.803428972151636	no association with either trait
PP.H1.abf	0.128323078245838	association with trait 1 but not with trait 2
PP.H2.abf	0.0528939231585165	association with trait 2 but not with trait 1
PP.H3.abf	0.00844126532987787	association with trait 1 and trait 2,two independent SNPs
PP.H4.abf	0.00691276111413178	association with trait 1 and trait 2, one shared SNP

pvalues in coloclization
		note
nsnps	583	NA
PP.H0.abf	4.52990830876848e-06	no association with either trait
PP.H1.abf	9.21861694069134e-07	association with trait 1 but not with trait 2
PP.H2.abf	0.0916212125783412	association with trait 2 but not with trait 1
PP.H3.abf	0.0177548110256025	association with trait 1 and trait 2,two independent SNPs
PP.H4.abf	0.890618524626053	association with trait 1 and trait 2, one shared SNP

pvalues in coloclization
		note
nsnps	281	NA
PP.H0.abf	2.77707888116324e-29	no association with either trait
PP.H1.abf	2.10073251325066e-30	association with trait 1 but not with trait 2
PP.H2.abf	0.395264611924459	association with trait 2 but not with trait 1
PP.H3.abf	0.029324540040624	association with trait 1 and trait 2,two independent SNPs
PP.H4.abf	0.575410848034918	association with trait 1 and trait 2, one shared SNP

Ulcerative colitist

pvalues in coloclization
		note
nsnps	466	NA
PP.H0.abf	6.36858252526649e-12	no association with either trait
PP.H1.abf	1.25749787143433e-12	association with trait 1 but not with trait 2
PP.H2.abf	0.76638668186091	association with trait 2 but not with trait 1
PP.H3.abf	0.151243237668553	association with trait 1 and trait 2,two independent SNPs
PP.H4.abf	0.0823700804629126	association with trait 1 and trait 2, one shared SNP

pvalues in coloclization
		note
nsnps	484	NA
PP.H0.abf	2.39875722879442e-07	no association with either trait
PP.H1.abf	1.58234762077974e-08	association with trait 1 but not with trait 2
PP.H2.abf	0.871084985071383	association with trait 2 but not with trait 1
PP.H3.abf	0.0573898654077472	association with trait 1 and trait 2,two independent SNPs
PP.H4.abf	0.0715248938216703	association with trait 1 and trait 2, one shared SNP

granulocyte count

lv74

pvalues in coloclization
		note
nsnps	807	NA
PP.H0.abf	0.000243730196779536	no association with either trait
PP.H1.abf	0.000165248082383001	association with trait 1 but not with trait 2
PP.H2.abf	0.115588213386481	association with trait 2 but not with trait 1
PP.H3.abf	0.077561897771207	association with trait 1 and trait 2,two independent SNPs
PP.H4.abf	0.80644091056315	association with trait 1 and trait 2, one shared SNP

pvalues in coloclization
		note
nsnps	786	NA
PP.H0.abf	3.19604103017961e-12	no association with either trait
PP.H1.abf	1.03593792505706e-11	association with trait 1 but not with trait 2
PP.H2.abf	0.014003650916366	association with trait 2 but not with trait 1
PP.H3.abf	0.0444487115504494	association with trait 1 and trait 2,two independent SNPs
PP.H4.abf	0.94154763751963	association with trait 1 and trait 2, one shared SNP

pvalues in coloclization
		note
nsnps	510	NA
PP.H0.abf	1.82259340012189e-17	no association with either trait
PP.H1.abf	1.92483992741527e-17	association with trait 1 but not with trait 2
PP.H2.abf	0.0297496892787095	association with trait 2 but not with trait 1
PP.H3.abf	0.030478859686348	association with trait 1 and trait 2,two independent SNPs
PP.H4.abf	0.939771451034946	association with trait 1 and trait 2, one shared SNP

pvalues in coloclization
		note
nsnps	510	NA
PP.H0.abf	1.82259340012189e-17	no association with either trait
PP.H1.abf	1.92483992741527e-17	association with trait 1 but not with trait 2
PP.H2.abf	0.0297496892787095	association with trait 2 but not with trait 1
PP.H3.abf	0.030478859686348	association with trait 1 and trait 2,two independent SNPs
PP.H4.abf	0.939771451034946	association with trait 1 and trait 2, one shared SNP

pvalues in coloclization
		note
nsnps	172	NA
PP.H0.abf	1.69067886793852e-46	no association with either trait
PP.H1.abf	5.78786302442303e-48	association with trait 1 but not with trait 2
PP.H2.abf	0.249934649969975	association with trait 2 but not with trait 1
PP.H3.abf	0.00781400109211381	association with trait 1 and trait 2,two independent SNPs
PP.H4.abf	0.742251348937904	association with trait 1 and trait 2, one shared SNP

LDL

lv35

pvalues in coloclization
		note
nsnps	150	NA
PP.H0.abf	1.14243004211355e-21	no association with either trait
PP.H1.abf	4.88169641330046e-23	association with trait 1 but not with trait 2
PP.H2.abf	0.914923549379037	association with trait 2 but not with trait 1
PP.H3.abf	0.039049399756932	association with trait 1 and trait 2,two independent SNPs
PP.H4.abf	0.04602705086403	association with trait 1 and trait 2, one shared SNP

pvalues in coloclization
		note
nsnps	80	NA
PP.H0.abf	2.38940663497786e-14	no association with either trait
PP.H1.abf	7.2663269498117e-15	association with trait 1 but not with trait 2
PP.H2.abf	0.594951780945732	association with trait 2 but not with trait 1
PP.H3.abf	0.180704012500906	association with trait 1 and trait 2,two independent SNPs
PP.H4.abf	0.224344206553332	association with trait 1 and trait 2, one shared SNP

lymphocyte count

lv74

pvalues in coloclization
		note
nsnps	786	NA
PP.H0.abf	1.7445088448985e-35	no association with either trait
PP.H1.abf	5.65450460730246e-35	association with trait 1 but not with trait 2
PP.H2.abf	0.0120008783933029	association with trait 2 but not with trait 1
PP.H3.abf	0.0379485898305526	association with trait 1 and trait 2,two independent SNPs
PP.H4.abf	0.950050531776139	association with trait 1 and trait 2, one shared SNP

pvalues in coloclization
		note
nsnps	510	NA
PP.H0.abf	1.07493786039491e-42	no association with either trait
PP.H1.abf	1.13524130672266e-42	association with trait 1 but not with trait 2
PP.H2.abf	0.0295868451797152	association with trait 2 but not with trait 1
PP.H3.abf	0.030306544960568	association with trait 1 and trait 2,two independent SNPs
PP.H4.abf	0.940106609859711	association with trait 1 and trait 2, one shared SNP

pvalues in coloclization
		note
nsnps	56	NA
PP.H0.abf	3.43436637262214e-46	no association with either trait
PP.H1.abf	2.92432501543514e-47	association with trait 1 but not with trait 2
PP.H2.abf	0.0605874640743969	association with trait 2 but not with trait 1
PP.H3.abf	0.00422376684575926	association with trait 1 and trait 2,two independent SNPs
PP.H4.abf	0.935188769079843	association with trait 1 and trait 2, one shared SNP

pvalues in coloclization
		note
nsnps	151	NA
PP.H0.abf	0.909367744368301	no association with either trait
PP.H1.abf	0.0805535049356063	association with trait 1 but not with trait 2
PP.H2.abf	0.00659955289120895	association with trait 2 but not with trait 1
PP.H3.abf	0.000581703311602042	association with trait 1 and trait 2,two independent SNPs
PP.H4.abf	0.00289749449328192	association with trait 1 and trait 2, one shared SNP

neutrophil count

pvalues in coloclization
		note
nsnps	807	NA
PP.H0.abf	0.000214294779531181	no association with either trait
PP.H1.abf	0.000145290989176229	association with trait 1 but not with trait 2
PP.H2.abf	0.117951543823456	association with trait 2 but not with trait 1
PP.H3.abf	0.079168146384457	association with trait 1 and trait 2,two independent SNPs
PP.H4.abf	0.80252072402338	association with trait 1 and trait 2, one shared SNP

pvalues in coloclization
		note
nsnps	786	NA
PP.H0.abf	2.82528454381721e-09	no association with either trait
PP.H1.abf	9.15764028177483e-09	association with trait 1 but not with trait 2
PP.H2.abf	0.0153647114415028	association with trait 2 but not with trait 1
PP.H3.abf	0.048866117423375	association with trait 1 and trait 2,two independent SNPs
PP.H4.abf	0.935769159152199	association with trait 1 and trait 2, one shared SNP

pvalues in coloclization
		note
nsnps	510	NA
PP.H0.abf	1.44966591128561e-13	no association with either trait
PP.H1.abf	1.53099140338639e-13	association with trait 1 but not with trait 2
PP.H2.abf	0.0296802594352	association with trait 2 but not with trait 1
PP.H3.abf	0.0304053919677193	association with trait 1 and trait 2,two independent SNPs
PP.H4.abf	0.939914348596783	association with trait 1 and trait 2, one shared SNP

pvalues in coloclization
		note
nsnps	56	NA
PP.H0.abf	1.5259694149023e-14	no association with either trait
PP.H1.abf	1.29934609433665e-15	association with trait 1 but not with trait 2
PP.H2.abf	0.0596791572833565	association with trait 2 but not with trait 1
PP.H3.abf	0.00414543889146503	association with trait 1 and trait 2,two independent SNPs
PP.H4.abf	0.936175403825163	association with trait 1 and trait 2, one shared SNP

pvalues in coloclization
		note
nsnps	172	NA
PP.H0.abf	9.90493571701678e-41	no association with either trait
PP.H1.abf	3.39085158529905e-42	association with trait 1 but not with trait 2
PP.H2.abf	0.262118676406559	association with trait 2 but not with trait 1
PP.H3.abf	0.00824372229545226	association with trait 1 and trait 2,two independent SNPs
PP.H4.abf	0.729637601297983	association with trait 1 and trait 2, one shared SNP

myeloid white cell count

pvalues in coloclization
		note
nsnps	807	NA
PP.H0.abf	0.000126242289634006	no association with either trait
PP.H1.abf	8.5591759056958e-05	association with trait 1 but not with trait 2
PP.H2.abf	0.112136433902647	association with trait 2 but not with trait 1
PP.H3.abf	0.0752156101050989	association with trait 1 and trait 2,two independent SNPs
PP.H4.abf	0.812436121943563	association with trait 1 and trait 2, one shared SNP

pvalues in coloclization
		note
nsnps	786	NA
PP.H0.abf	1.06923834059985e-14	no association with either trait
PP.H1.abf	3.46573944919043e-14	association with trait 1 but not with trait 2
PP.H2.abf	0.0134520292367394	association with trait 2 but not with trait 1
PP.H3.abf	0.0426583893747474	association with trait 1 and trait 2,two independent SNPs
PP.H4.abf	0.943889581388469	association with trait 1 and trait 2, one shared SNP

pvalues in coloclization
		note
nsnps	510	NA
PP.H0.abf	2.39167301496117e-20	no association with either trait
PP.H1.abf	2.52584460813423e-20	association with trait 1 but not with trait 2
PP.H2.abf	0.0296523673059772	association with trait 2 but not with trait 1
PP.H3.abf	0.0303758776983773	association with trait 1 and trait 2,two independent SNPs
PP.H4.abf	0.939971754995643	association with trait 1 and trait 2, one shared SNP

pvalues in coloclization
		note
nsnps	56	NA
PP.H0.abf	1.68997869196331e-22	no association with either trait
PP.H1.abf	1.43899818139885e-23	association with trait 1 but not with trait 2
PP.H2.abf	0.0589076369402022	association with trait 2 but not with trait 1
PP.H3.abf	0.00407890673429991	association with trait 1 and trait 2,two independent SNPs
PP.H4.abf	0.937013456325495	association with trait 1 and trait 2, one shared SNP

pvalues in coloclization
		note
nsnps	151	NA
PP.H0.abf	0.908607813893165	no association with either trait
PP.H1.abf	0.0804861888650081	association with trait 1 but not with trait 2
PP.H2.abf	0.00680067114563086	association with trait 2 but not with trait 1
PP.H3.abf	0.000598909823017954	association with trait 1 and trait 2,two independent SNPs
PP.H4.abf	0.00350641627317808	association with trait 1 and trait 2, one shared SNP

pvalues in coloclization
		note
nsnps	740	NA
PP.H0.abf	0.696244518692255	no association with either trait
PP.H1.abf	0.241303199421013	association with trait 1 but not with trait 2
PP.H2.abf	0.0295609541707098	association with trait 2 but not with trait 1
PP.H3.abf	0.0102225146358729	association with trait 1 and trait 2,two independent SNPs
PP.H4.abf	0.0226688130801494	association with trait 1 and trait 2, one shared SNP

red blood cell count

pvalues in coloclization
		note
nsnps	1	NA
PP.H0.abf	0.999890377109835	no association with either trait
PP.H1.abf	5.59464824756157e-05	association with trait 1 but not with trait 2
PP.H2.abf	5.08322124194453e-05	association with trait 2 but not with trait 1
PP.H3.abf	0	association with trait 1 and trait 2,two independent SNPs
PP.H4.abf	2.84419527022698e-06	association with trait 1 and trait 2, one shared SNP

pvalues in coloclization
		note
nsnps	434	NA
PP.H0.abf	0.884468683582122	no association with either trait
PP.H1.abf	0.0929659932493666	association with trait 1 but not with trait 2
PP.H2.abf	0.0163931929316615	association with trait 2 but not with trait 1
PP.H3.abf	0.00171862555024174	association with trait 1 and trait 2,two independent SNPs
PP.H4.abf	0.00445350468660804	association with trait 1 and trait 2, one shared SNP

sessionInfo()

R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)

Matrix products: default
BLAS/LAPACK: /software/openblas-0.2.19-el7-x86_64/lib/libopenblas_haswellp-r0.2.19.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] workflowr_1.6.2

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.5        rstudioapi_0.11   whisker_0.3-2     knitr_1.30       
 [5] magrittr_1.5      R6_2.4.1          rlang_0.4.8       highr_0.8        
 [9] stringr_1.4.0     tools_3.6.1       DT_0.15           xfun_0.18        
[13] git2r_0.26.1      crosstalk_1.1.0.1 htmltools_0.5.0   ellipsis_0.3.1   
[17] rprojroot_1.3-2   yaml_2.2.1        digest_0.6.25     tibble_3.0.3     
[21] lifecycle_0.2.0   crayon_1.3.4      later_1.1.0.1     htmlwidgets_1.5.2
[25] vctrs_0.3.4       promises_1.1.1    fs_1.5.0          glue_1.4.2       
[29] evaluate_0.14     rmarkdown_1.13    stringi_1.5.3     compiler_3.6.1   
[33] pillar_1.4.6      backports_1.1.10  jsonlite_1.7.1    httpuv_1.5.1     
[37] pkgconfig_2.0.3

absolute	relative
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/project2/xinhe/xsun/website/factor_analysis/output/info_pval5e8_pliercanon_ld_d1k_ageco_adp.rdata	output/info_pval5e8_pliercanon_ld_d1k_ageco_adp.rdata
/project2/xinhe/xsun/website/factor_analysis/output/lv74top025_pliercanon_adp.rdata	output/lv74top025_pliercanon_adp.rdata
/project2/xinhe/xsun/website/factor_analysis/output/lv84top025_pliercanon_adp.rdata	output/lv84top025_pliercanon_adp.rdata
/project2/xinhe/xsun/website/factor_analysis/output/lv121top025_pliercanon_adp.rdata	output/lv121top025_pliercanon_adp.rdata
/project2/xinhe/xsun/website/factor_analysis/output/lv29top025_pliercanon_adp.rdata	output/lv29top025_pliercanon_adp.rdata
/project2/xinhe/xsun/website/factor_analysis/output/lv35top025_pliercanon_adp.rdata	output/lv35top025_pliercanon_adp.rdata
/project2/xinhe/xsun/website/factor_analysis/output/lv104top025_pliercanon_adp.rdata	output/lv104top025_pliercanon_adp.rdata
/project2/xinhe/xsun/website/factor_analysis/output/eo_74_26498530.coloc.results_adp.rdata	output/eo_74_26498530.coloc.results_adp.rdata
/project2/xinhe/xsun/website/factor_analysis/output/eo_74_26521207.coloc.results_adp.rdata	output/eo_74_26521207.coloc.results_adp.rdata
/project2/xinhe/xsun/website/factor_analysis/output/eo_74_27970706.coloc.results_adp.rdata	output/eo_74_27970706.coloc.results_adp.rdata
/project2/xinhe/xsun/website/factor_analysis/output/eo_74_28986516.coloc.results_adp.rdata	output/eo_74_28986516.coloc.results_adp.rdata
/project2/xinhe/xsun/website/factor_analysis/output/eo_74_30331468.coloc.results_adp.rdata	output/eo_74_30331468.coloc.results_adp.rdata
/project2/xinhe/xsun/website/factor_analysis/output/eo_84_132280681.coloc.results_adp.rdata	output/eo_84_132280681.coloc.results_adp.rdata
/project2/xinhe/xsun/website/factor_analysis/output/eo_84_132395414.coloc.results_adp.rdata	output/eo_84_132395414.coloc.results_adp.rdata
/project2/xinhe/xsun/website/factor_analysis/output/eo_121_233205886.coloc.results_adp.rdata	output/eo_121_233205886.coloc.results_adp.rdata
/project2/xinhe/xsun/website/factor_analysis/output/eo_121_23520972.coloc.results_adp.rdata	output/eo_121_23520972.coloc.results_adp.rdata
/project2/xinhe/xsun/website/factor_analysis/output/eo_121_96350497.coloc.results_adp.rdata	output/eo_121_96350497.coloc.results_adp.rdata
/project2/xinhe/xsun/website/factor_analysis/output/EUR.UC_29_206798727.coloc.results_adp.rdata	output/EUR.UC_29_206798727.coloc.results_adp.rdata
/project2/xinhe/xsun/website/factor_analysis/output/EUR.UC_29_32836793.coloc.results_adp.rdata	output/EUR.UC_29_32836793.coloc.results_adp.rdata
/project2/xinhe/xsun/website/factor_analysis/output/gran_74_157050529.coloc.results_adp.rdata	output/gran_74_157050529.coloc.results_adp.rdata
/project2/xinhe/xsun/website/factor_analysis/output/gran_74_26463347.coloc.results_adp.rdata	output/gran_74_26463347.coloc.results_adp.rdata
/project2/xinhe/xsun/website/factor_analysis/output/gran_74_27873148.coloc.results_adp.rdata	output/gran_74_27873148.coloc.results_adp.rdata
/project2/xinhe/xsun/website/factor_analysis/output/gran_74_31276269.coloc.results_adp.rdata	output/gran_74_31276269.coloc.results_adp.rdata
/project2/xinhe/xsun/website/factor_analysis/output/LDL_35_20816003.coloc.results_adp.rdata	output/LDL_35_20816003.coloc.results_adp.rdata
/project2/xinhe/xsun/website/factor_analysis/output/LDL_35_45149969.coloc.results_adp.rdata	output/LDL_35_45149969.coloc.results_adp.rdata
/project2/xinhe/xsun/website/factor_analysis/output/lymph_74_26463347.coloc.results_adp.rdata	output/lymph_74_26463347.coloc.results_adp.rdata
/project2/xinhe/xsun/website/factor_analysis/output/lymph_74_27873148.coloc.results_adp.rdata	output/lymph_74_27873148.coloc.results_adp.rdata
/project2/xinhe/xsun/website/factor_analysis/output/lymph_74_28894720.coloc.results_adp.rdata	output/lymph_74_28894720.coloc.results_adp.rdata
/project2/xinhe/xsun/website/factor_analysis/output/lymph_74_30331468.coloc.results_adp.rdata	output/lymph_74_30331468.coloc.results_adp.rdata
/project2/xinhe/xsun/website/factor_analysis/output/neut_74_157050529.coloc.results_adp.rdata	output/neut_74_157050529.coloc.results_adp.rdata
/project2/xinhe/xsun/website/factor_analysis/output/neut_74_26463347.coloc.results_adp.rdata	output/neut_74_26463347.coloc.results_adp.rdata
/project2/xinhe/xsun/website/factor_analysis/output/neut_74_27873148.coloc.results_adp.rdata	output/neut_74_27873148.coloc.results_adp.rdata
/project2/xinhe/xsun/website/factor_analysis/output/neut_74_28894720.coloc.results_adp.rdata	output/neut_74_28894720.coloc.results_adp.rdata
/project2/xinhe/xsun/website/factor_analysis/output/neut_74_31276269.coloc.results_adp.rdata	output/neut_74_31276269.coloc.results_adp.rdata
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/project2/xinhe/xsun/website/factor_analysis/output/myeloid_wbc_74_30331468.coloc.results_adp.rdata	output/myeloid_wbc_74_30331468.coloc.results_adp.rdata
/project2/xinhe/xsun/website/factor_analysis/output/myeloid_wbc_74_5280229.coloc.results_adp.rdata	output/myeloid_wbc_74_5280229.coloc.results_adp.rdata
/project2/xinhe/xsun/website/factor_analysis/output/rbc_104_31149298.coloc.results_adp.rdata	output/rbc_104_31149298.coloc.results_adp.rdata
/project2/xinhe/xsun/website/factor_analysis/output/rbc_104_47092874.coloc.results_adp.rdata	output/rbc_104_47092874.coloc.results_adp.rdata

catalog_gwas_pliercanon_sep_ldclumping_r01d1000_adipose_sub

XSun

2020-11-19

Introduction

Material and Methods

Snps after filter

Results - pval < 5e-8 & 120 PEER factors & covariants: 10 PCs + GTEx:Sequencing platform,Sequencing protocol,Sex + AGE

Summary table

Info table

Enrichment analysis

Effect size plots

Asthma_2

BMI

Eosinophil count

Crohn’s disease

IBD

Ulcerative colitist

granulocyte count

HDL

LDL

lymphocyte count

myeloid white cell count

neutrophil count

plt

rbc

T2D_2

T2D

asthma

wbc

eo

Resampling

Eosinophil count

Ulcerative colitist

granulocyte count

LDL

lymphocyte count

neutrophil count

myeloid white cell count

red blood cell count

Effect size plots- more SNPs

Eosinophil count

Ulcerative colitist

granulocyte count

LDL

lymphocyte count

neutrophil count

myeloid white cell count

red blood cell count

Effect size plots - checking the reverse causality

Eosinophil count

Ulcerative colitist

granulocyte count

LDL

lymphocyte count

neutrophil count

myeloid white cell count

red blood cell count

QQplots - promising pairs

Eosinophil count

Ulcerative colitist

granulocyte count

LDL

lymphocyte count

neutrophil count

myeloid white cell count

red blood cell count

Colocalization

Eosinophil count

Ulcerative colitist

granulocyte count

LDL

lymphocyte count

neutrophil count

myeloid white cell count

red blood cell count